An understanding of chromosome biology is an essential for any model genetic system. Physical mapping can be accomplished using large insert libraries and repeated hybridization analysis. Recently applications of FISH technology (fluorescent in-situ hybridization) for chromosome identification and gene mapping have rejuvenated cytological Investigations. Chlamydomonas is a model genetic system to study photosynthesis and basal body organization. Currently there is no reliable high-throughput system to visualize Chlamydomonas chromosomes. We propose to use a combination of cytological techniques to develop a high-resolution "cytogenomic" view of the Chlamydomonas reinhardtii genome. We propose to develop a molecular karyotype, and to establish a firm chromosome number for this species. Additionally by using both pachytene chromosomes and extended DNA fibers as targets for our cytogenomic analyses, we will be able to develop a core set of chromosome specific cytogenetic markers (CSCMs) that will anchor the current linkage map to the entire array of chromosomes. We will investigate other genome wide events such as transfer of organellar DNA into the nuclear genome, and the size of chromosomal landmarks (rDNA and repetitive elements). Lastly, because of the widespread variation in chromosome number across Chlamydomonas species, we will use comparative cytogenomics to begin to look across different Chlamydomonas species for both hypervariable and highly conserved regions of the genome.